RT Journal Article
SR Electronic
T1 GAVIN - Gene-Aware Variant INterpretation for medical sequencing
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 072330
DO 10.1101/072330
A1 K. Joeri van der Velde
A1 Eddy N. de Boer
A1 Cleo C. van Diemen
A1 Birgit Sikkema-Raddatz
A1 Kristin M. Abbott
A1 Alain Knopperts
A1 Lude Franke
A1 Rolf H. Sijmons
A1 Tom J. de Koning
A1 Cisca Wijmenga
A1 Richard J. Sinke
A1 Morris A. Swertz
YR 2016
UL http://biorxiv.org/content/early/2016/08/30/072330.abstract
AB Here, we present GAVIN, a new method that delivers accurate classification of variants for next-generation sequencing molecular diagnostics. It is based on gene-specific calibrations of allele frequencies (from the ExAC database), effect impact (using SnpEff) and estimated deleteriousness (CADD scores) for >3,000 genes. In a benchmark on 18 clinical gene sets, we achieved a sensitivity of 91.6%, with a specificity of 78.2%. This accuracy was unmatched by 12 other tools we tested. We provide GAVIN as an online MOLGENIS service to annotate VCF files, and as open source executable for use in bioinformatic pipelines. It can be found at http://molgenis.org/gavin.